data_4LYF # _model_server_result.job_id iF6kNn4yP_eD9xj0KlYR9Q _model_server_result.datetime_utc '2024-10-15 16:20:45' _model_server_result.server_version 0.9.12 _model_server_result.query_name ligand _model_server_result.source_id pdb-bcif _model_server_result.entry_id 4lyf # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":202}' # _entry.id 4LYF # _exptl.entry_id 4LYF _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 443.201 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "GUANOSINE-5'-DIPHOSPHATE" _entity.pdbx_number_of_molecules 3 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 110.9 _cell.angle_gamma 90 _cell.entry_id 4LYF _cell.length_a 68.265 _cell.length_b 83.835 _cell.length_c 86.186 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4LYF _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I,J _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1 _pdbx_struct_oper_list.matrix[1][2] 0 _pdbx_struct_oper_list.matrix[1][3] 0 _pdbx_struct_oper_list.matrix[2][1] 0 _pdbx_struct_oper_list.matrix[2][2] 1 _pdbx_struct_oper_list.matrix[2][3] 0 _pdbx_struct_oper_list.matrix[3][1] 0 _pdbx_struct_oper_list.matrix[3][2] 0 _pdbx_struct_oper_list.matrix[3][3] 1 _pdbx_struct_oper_list.vector[1] 0 _pdbx_struct_oper_list.vector[2] 0 _pdbx_struct_oper_list.vector[3] 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 D N N ? 2 F N N ? 2 G N N # _struct_conn.conn_type_id covale _struct_conn.details ? _struct_conn.id covale1 _struct_conn.ptnr1_label_asym_id B _struct_conn.ptnr1_label_atom_id SG _struct_conn.ptnr1_label_comp_id CYS _struct_conn.ptnr1_label_seq_id 13 _struct_conn.ptnr1_auth_asym_id B _struct_conn.ptnr1_auth_comp_id CYS _struct_conn.ptnr1_auth_seq_id 12 _struct_conn.ptnr1_symmetry 1_555 _struct_conn.ptnr2_label_asym_id E _struct_conn.ptnr2_label_atom_id C18 _struct_conn.ptnr2_label_comp_id 21C _struct_conn.ptnr2_label_seq_id . _struct_conn.ptnr2_auth_asym_id B _struct_conn.ptnr2_auth_comp_id 21C _struct_conn.ptnr2_auth_seq_id 201 _struct_conn.ptnr2_symmetry 1_555 _struct_conn.pdbx_ptnr1_PDB_ins_code ? _struct_conn.pdbx_ptnr1_label_alt_id ? _struct_conn.pdbx_ptnr1_standard_comp_id ? _struct_conn.pdbx_ptnr2_PDB_ins_code ? _struct_conn.pdbx_ptnr2_label_alt_id ? _struct_conn.pdbx_ptnr3_PDB_ins_code ? _struct_conn.pdbx_ptnr3_label_alt_id ? _struct_conn.pdbx_ptnr3_label_asym_id ? _struct_conn.pdbx_ptnr3_label_atom_id ? _struct_conn.pdbx_ptnr3_label_comp_id ? _struct_conn.pdbx_ptnr3_label_seq_id ? _struct_conn.pdbx_PDB_id ? _struct_conn.pdbx_dist_value 1.831 _struct_conn.pdbx_value_order ? # _chem_comp.formula 'C10 H15 N5 O11 P2' _chem_comp.formula_weight 443.201 _chem_comp.id GDP _chem_comp.mon_nstd_flag n _chem_comp.name "GUANOSINE-5'-DIPHOSPHATE" _chem_comp.type 'rna linking' _chem_comp.pdbx_synonyms ? # _atom_sites.entry_id 4LYF _atom_sites.fract_transf_matrix[1][1] 0.014649 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.005594 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.011928 _atom_sites.fract_transf_matrix[2][3] 0 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 0.01242 _atom_sites.fract_transf_vector[1] 0 _atom_sites.fract_transf_vector[2] 0 _atom_sites.fract_transf_vector[3] 0 # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_ins_code D 2 GDP A 1 201 220 GDP GDP . E 3 21C B 1 201 210 21C LIG . F 2 GDP B 1 202 220 GDP GDP . G 2 GDP C 1 201 220 GDP GDP . H 4 HOH A 1 301 1 HOH HOH . H 4 HOH A 2 302 2 HOH HOH . H 4 HOH A 3 303 6 HOH HOH . H 4 HOH A 4 304 7 HOH HOH . H 4 HOH A 5 305 15 HOH HOH . H 4 HOH A 6 306 16 HOH HOH . H 4 HOH A 7 307 19 HOH HOH . H 4 HOH A 8 308 25 HOH HOH . H 4 HOH A 9 309 30 HOH HOH . H 4 HOH A 10 310 35 HOH HOH . H 4 HOH A 11 311 36 HOH HOH . H 4 HOH A 12 312 39 HOH HOH . H 4 HOH A 13 313 41 HOH HOH . H 4 HOH A 14 314 42 HOH HOH . H 4 HOH A 15 315 44 HOH HOH . H 4 HOH A 16 316 45 HOH HOH . H 4 HOH A 17 317 46 HOH HOH . H 4 HOH A 18 318 55 HOH HOH . H 4 HOH A 19 319 56 HOH HOH . H 4 HOH A 20 320 58 HOH HOH . H 4 HOH A 21 321 59 HOH HOH . H 4 HOH A 22 322 62 HOH HOH . H 4 HOH A 23 323 63 HOH HOH . H 4 HOH A 24 324 65 HOH HOH . H 4 HOH A 25 325 68 HOH HOH . H 4 HOH A 26 326 71 HOH HOH . H 4 HOH A 27 327 72 HOH HOH . H 4 HOH A 28 328 79 HOH HOH . H 4 HOH A 29 329 81 HOH HOH . H 4 HOH A 30 330 82 HOH HOH . H 4 HOH A 31 331 83 HOH HOH . H 4 HOH A 32 332 84 HOH HOH . H 4 HOH A 33 333 86 HOH HOH . H 4 HOH A 34 334 91 HOH HOH . H 4 HOH A 35 335 93 HOH HOH . H 4 HOH A 36 336 95 HOH HOH . H 4 HOH A 37 337 98 HOH HOH . H 4 HOH A 38 338 101 HOH HOH . H 4 HOH A 39 339 102 HOH HOH . H 4 HOH A 40 340 103 HOH HOH . H 4 HOH A 41 341 104 HOH HOH . H 4 HOH A 42 342 112 HOH HOH . H 4 HOH A 43 343 114 HOH HOH . H 4 HOH A 44 344 115 HOH HOH . H 4 HOH A 45 345 117 HOH HOH . H 4 HOH A 46 346 123 HOH HOH . H 4 HOH A 47 347 125 HOH HOH . H 4 HOH A 48 348 126 HOH HOH . H 4 HOH A 49 349 129 HOH HOH . H 4 HOH A 50 350 131 HOH HOH . H 4 HOH A 51 351 132 HOH HOH . H 4 HOH A 52 352 133 HOH HOH . H 4 HOH A 53 353 138 HOH HOH . H 4 HOH A 54 354 139 HOH HOH . H 4 HOH A 55 355 140 HOH HOH . H 4 HOH A 56 356 147 HOH HOH . H 4 HOH A 57 357 152 HOH HOH . H 4 HOH A 58 358 154 HOH HOH . H 4 HOH A 59 359 155 HOH HOH . H 4 HOH A 60 360 156 HOH HOH . H 4 HOH A 61 361 157 HOH HOH . H 4 HOH A 62 362 158 HOH HOH . H 4 HOH A 63 363 162 HOH HOH . H 4 HOH A 64 364 163 HOH HOH . H 4 HOH A 65 365 165 HOH HOH . H 4 HOH A 66 366 169 HOH HOH . H 4 HOH A 67 367 172 HOH HOH . H 4 HOH A 68 368 179 HOH HOH . H 4 HOH A 69 369 184 HOH HOH . H 4 HOH A 70 370 187 HOH HOH . H 4 HOH A 71 371 189 HOH HOH . H 4 HOH A 72 372 193 HOH HOH . H 4 HOH A 73 373 194 HOH HOH . H 4 HOH A 74 374 195 HOH HOH . I 4 HOH B 1 301 3 HOH HOH . I 4 HOH B 2 302 4 HOH HOH . I 4 HOH B 3 303 8 HOH HOH . I 4 HOH B 4 304 9 HOH HOH . I 4 HOH B 5 305 11 HOH HOH . I 4 HOH B 6 306 12 HOH HOH . I 4 HOH B 7 307 17 HOH HOH . I 4 HOH B 8 308 20 HOH HOH . I 4 HOH B 9 309 22 HOH HOH . I 4 HOH B 10 310 24 HOH HOH . I 4 HOH B 11 311 26 HOH HOH . I 4 HOH B 12 312 32 HOH HOH . I 4 HOH B 13 313 33 HOH HOH . I 4 HOH B 14 314 34 HOH HOH . I 4 HOH B 15 315 37 HOH HOH . I 4 HOH B 16 316 38 HOH HOH . I 4 HOH B 17 317 40 HOH HOH . I 4 HOH B 18 318 48 HOH HOH . I 4 HOH B 19 319 49 HOH HOH . I 4 HOH B 20 320 50 HOH HOH . I 4 HOH B 21 321 53 HOH HOH . I 4 HOH B 22 322 54 HOH HOH . I 4 HOH B 23 323 57 HOH HOH . I 4 HOH B 24 324 64 HOH HOH . I 4 HOH B 25 325 66 HOH HOH . I 4 HOH B 26 326 67 HOH HOH . I 4 HOH B 27 327 69 HOH HOH . I 4 HOH B 28 328 70 HOH HOH . I 4 HOH B 29 329 76 HOH HOH . I 4 HOH B 30 330 78 HOH HOH . I 4 HOH B 31 331 80 HOH HOH . I 4 HOH B 32 332 88 HOH HOH . I 4 HOH B 33 333 89 HOH HOH . I 4 HOH B 34 334 99 HOH HOH . I 4 HOH B 35 335 105 HOH HOH . I 4 HOH B 36 336 107 HOH HOH . I 4 HOH B 37 337 108 HOH HOH . I 4 HOH B 38 338 109 HOH HOH . I 4 HOH B 39 339 111 HOH HOH . I 4 HOH B 40 340 118 HOH HOH . I 4 HOH B 41 341 124 HOH HOH . I 4 HOH B 42 342 128 HOH HOH . I 4 HOH B 43 343 130 HOH HOH . I 4 HOH B 44 344 135 HOH HOH . I 4 HOH B 45 345 143 HOH HOH . I 4 HOH B 46 346 144 HOH HOH . I 4 HOH B 47 347 145 HOH HOH . I 4 HOH B 48 348 146 HOH HOH . I 4 HOH B 49 349 149 HOH HOH . I 4 HOH B 50 350 150 HOH HOH . I 4 HOH B 51 351 153 HOH HOH . I 4 HOH B 52 352 159 HOH HOH . I 4 HOH B 53 353 160 HOH HOH . I 4 HOH B 54 354 161 HOH HOH . I 4 HOH B 55 355 168 HOH HOH . I 4 HOH B 56 356 170 HOH HOH . I 4 HOH B 57 357 173 HOH HOH . I 4 HOH B 58 358 175 HOH HOH . I 4 HOH B 59 359 176 HOH HOH . I 4 HOH B 60 360 178 HOH HOH . I 4 HOH B 61 361 180 HOH HOH . I 4 HOH B 62 362 181 HOH HOH . I 4 HOH B 63 363 183 HOH HOH . I 4 HOH B 64 364 185 HOH HOH . I 4 HOH B 65 365 186 HOH HOH . I 4 HOH B 66 366 188 HOH HOH . I 4 HOH B 67 367 190 HOH HOH . I 4 HOH B 68 368 191 HOH HOH . I 4 HOH B 69 369 192 HOH HOH . I 4 HOH B 70 370 196 HOH HOH . J 4 HOH C 1 301 5 HOH HOH . J 4 HOH C 2 302 10 HOH HOH . J 4 HOH C 3 303 13 HOH HOH . J 4 HOH C 4 304 14 HOH HOH . J 4 HOH C 5 305 18 HOH HOH . J 4 HOH C 6 306 21 HOH HOH . J 4 HOH C 7 307 23 HOH HOH . J 4 HOH C 8 308 27 HOH HOH . J 4 HOH C 9 309 28 HOH HOH . J 4 HOH C 10 310 29 HOH HOH . J 4 HOH C 11 311 31 HOH HOH . J 4 HOH C 12 312 43 HOH HOH . J 4 HOH C 13 313 47 HOH HOH . J 4 HOH C 14 314 51 HOH HOH . J 4 HOH C 15 315 52 HOH HOH . J 4 HOH C 16 316 60 HOH HOH . J 4 HOH C 17 317 61 HOH HOH . J 4 HOH C 18 318 73 HOH HOH . J 4 HOH C 19 319 74 HOH HOH . J 4 HOH C 20 320 75 HOH HOH . J 4 HOH C 21 321 77 HOH HOH . J 4 HOH C 22 322 85 HOH HOH . J 4 HOH C 23 323 87 HOH HOH . J 4 HOH C 24 324 90 HOH HOH . J 4 HOH C 25 325 92 HOH HOH . J 4 HOH C 26 326 94 HOH HOH . J 4 HOH C 27 327 96 HOH HOH . J 4 HOH C 28 328 97 HOH HOH . J 4 HOH C 29 329 100 HOH HOH . J 4 HOH C 30 330 106 HOH HOH . J 4 HOH C 31 331 110 HOH HOH . J 4 HOH C 32 332 113 HOH HOH . J 4 HOH C 33 333 116 HOH HOH . J 4 HOH C 34 334 119 HOH HOH . J 4 HOH C 35 335 120 HOH HOH . J 4 HOH C 36 336 121 HOH HOH . J 4 HOH C 37 337 122 HOH HOH . J 4 HOH C 38 338 127 HOH HOH . J 4 HOH C 39 339 134 HOH HOH . J 4 HOH C 40 340 136 HOH HOH . J 4 HOH C 41 341 137 HOH HOH . J 4 HOH C 42 342 141 HOH HOH . J 4 HOH C 43 343 142 HOH HOH . J 4 HOH C 44 344 148 HOH HOH . J 4 HOH C 45 345 151 HOH HOH . J 4 HOH C 46 346 164 HOH HOH . J 4 HOH C 47 347 166 HOH HOH . J 4 HOH C 48 348 167 HOH HOH . J 4 HOH C 49 349 171 HOH HOH . J 4 HOH C 50 350 174 HOH HOH . J 4 HOH C 51 351 177 HOH HOH . J 4 HOH C 52 352 182 HOH HOH . J 4 HOH C 53 353 197 HOH HOH . # loop_ _atom_site.group_PDB _atom_site.id _atom_site.type_symbol _atom_site.label_atom_id _atom_site.label_comp_id _atom_site.label_seq_id _atom_site.label_alt_id _atom_site.pdbx_PDB_ins_code _atom_site.label_asym_id _atom_site.label_entity_id _atom_site.Cartn_x _atom_site.Cartn_y _atom_site.Cartn_z _atom_site.occupancy _atom_site.B_iso_or_equiv _atom_site.pdbx_formal_charge _atom_site.auth_atom_id _atom_site.auth_comp_id _atom_site.auth_seq_id _atom_site.auth_asym_id _atom_site.pdbx_PDB_model_num HETATM 1 P PB GDP . . . F 2 14.695 11.157 25.979 1 22.98 ? PB GDP 202 B 1 HETATM 2 O O1B GDP . . . F 2 14.859 10.55 24.592 1 22.77 ? O1B GDP 202 B 1 HETATM 3 O O2B GDP . . . F 2 13.972 10.225 26.925 1 24.7 ? O2B GDP 202 B 1 HETATM 4 O O3B GDP . . . F 2 14.109 12.557 25.939 1 23.83 ? O3B GDP 202 B 1 HETATM 5 O O3A GDP . . . F 2 16.218 11.236 26.557 1 23.01 ? O3A GDP 202 B 1 HETATM 6 P PA GDP . . . F 2 16.952 12.381 27.428 1 24.69 ? PA GDP 202 B 1 HETATM 7 O O1A GDP . . . F 2 17.136 13.673 26.67 1 25.28 ? O1A GDP 202 B 1 HETATM 8 O O2A GDP . . . F 2 16.257 12.521 28.755 1 26.52 ? O2A GDP 202 B 1 HETATM 9 O O5' GDP . . . F 2 18.389 11.714 27.612 1 25.06 ? O5' GDP 202 B 1 HETATM 10 C C5' GDP . . . F 2 18.495 10.506 28.354 1 26.18 ? C5' GDP 202 B 1 HETATM 11 C C4' GDP . . . F 2 19.909 10.39 28.885 1 26.23 ? C4' GDP 202 B 1 HETATM 12 O O4' GDP . . . F 2 20.859 10.367 27.815 1 25.71 ? O4' GDP 202 B 1 HETATM 13 C C3' GDP . . . F 2 20.28 11.584 29.734 1 27.45 ? C3' GDP 202 B 1 HETATM 14 O O3' GDP . . . F 2 21.051 11.104 30.837 1 29.76 ? O3' GDP 202 B 1 HETATM 15 C C2' GDP . . . F 2 21.121 12.466 28.84 1 27.49 ? C2' GDP 202 B 1 HETATM 16 O O2' GDP . . . F 2 22.125 13.226 29.522 1 29.49 ? O2' GDP 202 B 1 HETATM 17 C C1' GDP . . . F 2 21.798 11.426 27.99 1 25.79 ? C1' GDP 202 B 1 HETATM 18 N N9 GDP . . . F 2 22.127 11.905 26.654 1 24.31 ? N9 GDP 202 B 1 HETATM 19 C C8 GDP . . . F 2 21.262 12.418 25.761 1 23.34 ? C8 GDP 202 B 1 HETATM 20 N N7 GDP . . . F 2 21.889 12.708 24.606 1 23.15 ? N7 GDP 202 B 1 HETATM 21 C C5 GDP . . . F 2 23.173 12.361 24.778 1 22.66 ? C5 GDP 202 B 1 HETATM 22 C C6 GDP . . . F 2 24.378 12.373 23.968 1 22.54 ? C6 GDP 202 B 1 HETATM 23 O O6 GDP . . . F 2 24.348 12.81 22.808 1 22.74 ? O6 GDP 202 B 1 HETATM 24 N N1 GDP . . . F 2 25.492 11.91 24.557 1 22.55 ? N1 GDP 202 B 1 HETATM 25 C C2 GDP . . . F 2 25.549 11.414 25.799 1 24.11 ? C2 GDP 202 B 1 HETATM 26 N N2 GDP . . . F 2 26.724 10.964 26.295 1 25.96 ? N2 GDP 202 B 1 HETATM 27 N N3 GDP . . . F 2 24.479 11.352 26.6 1 24.09 ? N3 GDP 202 B 1 HETATM 28 C C4 GDP . . . F 2 23.312 11.806 26.128 1 23.43 ? C4 GDP 202 B 1 HETATM 29 H H5' GDP . . . F 2 17.784 10.514 29.183 1 31.42 ? H5' GDP 202 B 1 HETATM 30 H "H5''" GDP . . . F 2 18.266 9.653 27.712 1 31.42 ? "H5''" GDP 202 B 1 HETATM 31 H H4' GDP . . . F 2 19.995 9.476 29.49 1 31.47 ? H4' GDP 202 B 1 HETATM 32 H H3' GDP . . . F 2 19.378 12.117 30.066 1 32.94 ? H3' GDP 202 B 1 HETATM 33 H HO3' GDP . . . F 2 21.306 11.848 31.4 1 35.71 ? HO3' GDP 202 B 1 HETATM 34 H H2' GDP . . . F 2 20.478 13.105 28.219 1 32.98 ? H2' GDP 202 B 1 HETATM 35 H HO2' GDP . . . F 2 21.701 13.858 30.119 1 35.39 ? HO2' GDP 202 B 1 HETATM 36 H H1' GDP . . . F 2 22.698 11.062 28.504 1 30.95 ? H1' GDP 202 B 1 HETATM 37 H H8 GDP . . . F 2 20.209 12.586 25.95 1 28.01 ? H8 GDP 202 B 1 HETATM 38 H HN1 GDP . . . F 2 26.369 11.911 23.998 1 27.06 ? HN1 GDP 202 B 1 HETATM 39 H HN21 GDP . . . F 2 26.767 10.596 27.234 1 31.16 ? HN21 GDP 202 B 1 HETATM 40 H HN22 GDP . . . F 2 27.555 10.987 25.722 1 31.16 ? HN22 GDP 202 B 1 # _model_server_stats.io_time_ms 39 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 9 _model_server_stats.query_time_ms 312 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 40 #